X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.21 α = 90
b = 56.66 β = 90
c = 66.13 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-13
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9763 ESRF ID14-4

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.4 42 99.89 0.047 -- -- 13.4 41043 40997 0.0 -3.0 12.45
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.4 1.47 98.3 0.227 0.227 3.6 12.5 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
RIP - Radiation-Damage Induced Phasing 1.4 41.89 -- 0.0 40997 40997 2061 99.89 0.13919 0.13919 0.13785 0.16464 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4 1.436 -- 150 2812 0.185 0.232 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic for protein and ligands. Water molecules are refined isotropic
Mean Isotropic B 14.343
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.147
r_scbond_it 3.388
r_gen_planes_refined 0.009
r_mcangle_it 2.566
r_sphericity_bonded 7.071
r_rigid_bond_restr 1.263
r_chiral_restr 0.123
r_dihedral_angle_1_deg 6.386
r_mcbond_it 1.608
r_nbd_refined 0.198
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.123
r_angle_refined_deg 1.626
r_scangle_it 4.5
r_symmetry_vdw_refined 0.165
r_sphericity_free 1.262
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 288

Software

Software
Software Name Purpose
ProDC data collection
SCALA data scaling
SHELXD phasing
SHARP phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)